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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Peru
Russia
Indonesia
United Kingdom
Italy
Colombia
France
Argentina
Iran
Germany
Spain
South Africa
Poland
Turkey
Ukraine
Chile
Romania
Philippines
Ecuador
Czechia
Hungary
Canada
Bangladesh
Pakistan
Belgium
Tunisia
Iraq
Bulgaria
Bolivia
Malaysia
Netherlands
Portugal
Egypt
Japan
Burma
Paraguay
Sweden
Kazakhstan
Greece
Vietnam
Morocco
Thailand
Slovakia
Guatemala
Switzerland
Nepal
Austria
Jordan
Sri Lanka
Bosnia and Herzegovina
Honduras
Saudi Arabia
Croatia
Lebanon
Georgia
Serbia
Israel
Afghanistan
Panama
Moldova
North Macedonia
Uruguay
Azerbaijan
Cuba
Costa Rica
Algeria
Ireland
Armenia
Kenya
Ethiopia
China
Lithuania
Zimbabwe
Slovenia
Libya
Venezuela
Oman
Dominican Republic
Belarus
West Bank and Gaza
Zambia
Namibia
Uganda
El Salvador
Sudan
Kosovo
Denmark
Latvia
Nigeria
Kyrgyzstan
Albania
Kuwait
South Korea
Botswana
Malawi
United Arab Emirates
Syria
Cambodia
Mozambique
Senegal
Montenegro
Jamaica
Bahrain
Cameroon
Trinidad and Tobago
Estonia
Angola
Eswatini
Rwanda
Uzbekistan
Ghana
Congo (Kinshasa)
Australia
Finland
Somalia
Mongolia
Madagascar
Taiwan*
Luxembourg
Norway
Suriname
Mauritania
Guyana
Qatar
Haiti
Mali
Fiji
Cyprus
Cote d'Ivoire
Malta
Bahamas
Lesotho
Belize
Guinea
Cabo Verde
Maldives
Hong Kong
Nicaragua
Togo
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Djibouti
Benin
Andorra
Tajikistan
South Sudan
Seychelles
Central African Republic

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Peru
Russia
Indonesia
United Kingdom
Italy
Colombia
France
Argentina
Iran
Germany
Spain
South Africa
Poland
Turkey
Ukraine
Chile
Romania
Philippines
Ecuador
Czechia
Hungary
Canada
Bangladesh
Pakistan
Belgium
Tunisia
Iraq
Bulgaria
Bolivia
Malaysia
Netherlands
Portugal
Egypt
Japan
Burma
Paraguay
Sweden
Kazakhstan
Greece
Vietnam
Morocco
Thailand
Slovakia
Guatemala
Switzerland
Nepal
Austria
Jordan
Sri Lanka
Bosnia and Herzegovina
Honduras
Saudi Arabia
Croatia
Lebanon
Georgia
Serbia
Israel
Afghanistan
Panama
Moldova
North Macedonia
Uruguay
Azerbaijan
Cuba
Costa Rica
Algeria
Ireland
Armenia
Kenya
Ethiopia
China
Lithuania
Zimbabwe
Slovenia
Libya
Venezuela
Oman
Dominican Republic
Belarus
West Bank and Gaza
Zambia
Namibia
Uganda
El Salvador
Sudan
Kosovo
Denmark
Latvia
Nigeria
Kyrgyzstan
Albania
Kuwait
South Korea
Botswana
Malawi
United Arab Emirates
Syria
Cambodia
Mozambique
Senegal
Montenegro
Jamaica
Bahrain
Cameroon
Trinidad and Tobago
Estonia
Angola
Eswatini
Rwanda
Uzbekistan
Ghana
Congo (Kinshasa)
Australia
Finland
Somalia
Mongolia
Madagascar
Taiwan*
Luxembourg
Norway
Suriname
Mauritania
Guyana
Qatar
Haiti
Mali
Fiji
Cyprus
Cote d'Ivoire
Malta
Bahamas
Lesotho
Belize
Guinea
Cabo Verde
Maldives
Hong Kong
Nicaragua
Togo
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Djibouti
Benin
Andorra
Tajikistan
South Sudan
Seychelles
Central African Republic